JOURNAL BROWSE
Search
Advanced SearchSearch Tips
OrCanome: a Comprehensive Resource for Oral Cancer
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
 Title & Authors
OrCanome: a Comprehensive Resource for Oral Cancer
Bhartiya, Deeksha; Kumar, Amit; Singh, Harpreet; Sharma, Amitesh; Kaushik, Anita; Kumari, Suchitra; Mehrotra, Ravi;
  PDF(new window)
 Abstract
Oral cancer is one of the most prevalent cancers in India but the underlying mechanisms are minimally unraveled. Cancer research has immensely benefited from genome scale high throughput studies which have contributed to expanding the volume of data. Such datasets also exist for oral cancer genes but there has been no consolidated approach to integrate the data to reveal meaningful biological information. OrCanome is one of the largest and comprehensive, user-friendly databases of oral cancer. It features a compilation of over 900 genes dysregulated in oral cancer and provides detailed annotations of the genes, transcripts and proteins along with additional information encompassing expression, inhibitors, epitopes and pathways. The resource has been envisioned as a one-stop solution for genomic, transcriptomic and proteomic annotation of these genes and the integrated approach will facilitate the identification of potential biomarkers and therapeutic targets.
 Keywords
Oral cancer;resource;annotation;genes;biomarkers;
 Language
English
 Cited by
 References
1.
Barrett T, Wilhite SE, Ledoux P, et al (2013). NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res, 41, D991-5. crossref(new window)

2.
Bento AP, Gaulton A, Hersey A, et al (2014). The ChEMBL bioactivity database: an update. Nucleic Acids Res, 42, 1083-90. crossref(new window)

3.
Berglund L, Bjorling E, Oksvold P, et al (2008). A genecentric Human Protein Atlas for expression profiles based on antibodies. Mol Cell Proteomics, 7, 2019-27. crossref(new window)

4.
Berman HM, Battistuz T, Bhat TN, et al (2002). The Protein Data Bank. Acta Crystallogr D Biol Crystallogr, 58, 899-907. crossref(new window)

5.
Burger MC (2015). ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics. J Cheminform, 7, 35. crossref(new window)

6.
Coelho KR (2012). Challenges of the oral cancer burden in India. J Cancer Epidemiol, 2012, 701932.

7.
Ferlay J, Soerjomataram I, Dikshit R, et al (2015). Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int J Cancer, 136, 359-86. crossref(new window)

8.
Flicek P, Amode MR, Barrell D, et al (2014). Ensembl 2014. Nucleic Acids Res, 42, 749-55. crossref(new window)

9.
Gadewal NS, Zingde SM (2011). Database and interaction network of genes involved in oral cancer: Version II. Bioinformation, 6, 169-70. crossref(new window)

10.
Hamosh A, Scott AF, Amberger JS, et al (2005). Online mendelian inheritance in man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res, 33, 514-7.

11.
Harrow J, Frankish A, Gonzalez JM, et al (2012). GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res, 22, 1760-74. crossref(new window)

12.
Huang da W, Sherman BT, Lempicki RA (2009a). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res, 37, 1-13. crossref(new window)

13.
Huang da W, Sherman BT, Lempicki RA (2009b). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc, 4, 44-57.

14.
Hunter S, Apweiler R, Attwood TK, et al (2009). InterPro: the integrative protein signature database. Nucleic Acids Res, 37, 211-5. crossref(new window)

15.
India Project Team of the International Cancer Genome Consortium (2013). Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrentlymutated genes and molecular subgroups. Nat Commun, 4, 2873.

16.
Kanehisa M, Goto S (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res, 28, 27-30. crossref(new window)

17.
Krogh A, Larsson B, von Heijne G, et al (2001). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol, 305, 567-80. crossref(new window)

18.
Lian Y, Ge M, Pan XM (2014). EPMLR: sequence-based linear B-cell epitope prediction method using multiple linear regression. BMC Bioinformatics, 15, 414. crossref(new window)

19.
Liu T, Lin Y, Wen X, et al (2007). BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res, 35, 198-201. crossref(new window)

20.
Mehrotra R, Gupta DK (2011). Exciting new advances in oral cancer diagnosis: avenues to early detection. Head Neck Oncol, 3, 33. crossref(new window)

21.
Mehrotra R, Yadav S (2006). Oral squamous cell carcinoma: etiology, pathogenesis and prognostic value of genomic alterations. Indian J Cancer, 43, 60-6. crossref(new window)

22.
Mitra S, Das S, Das S, et al (2012). HNOCDB: a comprehensive database of genes and miRNAs relevant to head and neck and oral cancer. Oral Oncol, 48, 117-9. crossref(new window)

23.
Nakagawa H, Wardell CP, Furuta M, et al (2015). Cancer wholegenome sequencing: present and future. Oncogene.

24.
O'Boyle NM, Banck M, James CA, et al (2011). Open Babel: An open chemical toolbox. J Cheminform, 3, 33. crossref(new window)

25.
Petryszak R, Burdett T, Fiorelli B, et al (2014). Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res, 42, 926-32. crossref(new window)

26.
Rajaraman P, Anderson BO, Basu P, et al (2015). Recommendations for screening and early detection of common cancers in India. Lancet Oncol, 16, 352-61. crossref(new window)

27.
Reis PP, Waldron L, Perez-Ordonez B, et al (2011). A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence. BMC Cancer, 11, 437. crossref(new window)

28.
Reuter JA, Spacek DV, Snyder MP (2015). High-throughput sequencing technologies. Mol Cell, 58, 586-97. crossref(new window)

29.
Saeed AA, Sims AH, Prime SS, et al (2015). Gene expression profiling reveals biological pathways responsible for phenotypic heterogeneity between UK and Sri Lankan oral squamous cell carcinomas. Oral Oncol, 51, 237-46. crossref(new window)

30.
Thariat J, Vignot S, Lapierre A, et al (2015). Integrating genomics in head and neck cancer treatment: promises and pitfalls. Crit Rev Oncol Hematol, 95, 397-406. crossref(new window)

31.
Uhlen M, Fagerberg L, Hallstrom BM, et al (2015). Proteomics. Tissue-based map of the human proteome. Science, 347, 1260419. crossref(new window)

32.
Uhlen M, Oksvold P, Fagerberg L, et al (2010). Towards a knowledge-based Human Protein Atlas. Nat Biotechnol, 28, 1248-50. crossref(new window)

33.
UniProt Consortium (2015). UniProt: a hub for protein information. Nucleic Acids Res, 43, 204-12. crossref(new window)